Since the ability of some cells to engulf particulate material was observed before Metchnikoff, he did not “discover” phagocytosis, as is sometimes mentioned in textbooks. Rather, he assigned to particle internalization the role of defending the host against noxious stimuli, which represented a new function relative to the previously recognized task of intracellular digestion. With this proposal, Metchnikoff built the conceptual framework within which immunity could finally be seen as an active host function triggered by noxious stimuli. In this sense, Metchnikoff can be rightly regarded as the father of all immunological sciences and not only of innate immunity or myeloid cell biology. Moreover, the recognition properties of his phagocyte fit surprisingly well with recent discoveries and modern models of immune sensing. For example, rather than assigning to immune recognition exclusively the function of eliminating nonself components (as others did after him), Metchnikoff viewed phagocytes as homeostatic agents capable of monitoring the internal environment and promoting tissue remodeling, thereby continuously defining the identity of the organism. No doubt, Metchnikoff’s life and creativity can provide, still today, a rich source of inspiration.

Fermentation has been used as a method of food preservation for millennia. Some modern food fermentations are still initiated using the indigenous bacterial micro-flora of the raw substrate, also referred to as spontaneous fermentation. From the nutrient-rich environments to extreme environments such as the human digestive tract or deep-ocean thermal vents, bacteriophages have been discovered. Bacteriophages are undoubtedly the greatest threat in fermented food productions, especially in the dairy industry, which has openly acknowledged this biotechnological problem. Starter cultures used by the dairy industry are composed of lactic acid bacteria, which represent a diverse group including, among others, the genera Lactococcus and Lactobacillus as well as the species Streptococcus thermophilus. The bacteriophages infecting these groups of bacteria have been extensively characterized because of their negative impact on the industry. For example, lactococcal phages are the most-studied group of bacterial viruses after the Escherichia coli phages. Biochemical methods are based primarily on immunochemical assays and molecular detection of bacteriophage genetic material (most often double-stranded DNA). Biochemical detection techniques are essential in identifying an emerging phage population. Bacteriophage-insensitive mutants (BIMs) have the same genetic determinants and most likely the same desired metabolic properties as the wild-type strain. Bacterial restriction-modification (R-M) systems are recognized as among the first line of defense after foreign DNA entry into the cell. The emergence of resistant phages points to the necessity of continuing to identify new phage resistance mechanisms for long-term phage resistance in important bioindustries.

Live microbes that when administered in adequate amounts confer a health benefit on the host are termed “probiotics”. Important contributing research includes using modern molecular methods to refine our understanding of the types and activities of microbes colonizing healthy and diseased humans; identifying the way in which microbes dynamically interact with host cells and other commensal microbes; applying functional genomics and gene array techniques to better understand the genetic and metabolic capacity of therapeutic microbes. By nature of their ability to influence the intestinal microbiota and environment, their physiological effects are often complementary to probiotic influences. Numerous are the types of health effects of probiotics and prebiotics supported by controlled (albeit some are preliminary) studies in the target host animal (humans, companion animals, or animals used in animal agriculture). The practical implications of such observations suggest the importance of testing blended strain products as they are in the final product formulation. With this caution in mind, it is of interest to note the list of health targets for the many different types of probiotics that have been tested in humans. Dissemination of such information is critical to providing a better understanding of the parameters for successful intervention for probiotics and prebiotics. Perhaps the most compelling means of probiotic function may be through interaction with host immune cells, which may occur during transit of the microbe through the sparsely colonized small intestine that is rich in immune sensing cells.

The emergence of antibiotic-resistant bacteria and natural ways of suppressing the growth of pathogens has contributed to the growth of probiotic foods and nutraceuticals. Probiotic bacteria not only compete and suppress “unhealthy fermentation” in the human intestine but also produce a number of beneficial health effects of their own. The viability of probiotics has been both a marketing and a technological challenge for many processing industries. Viability during the shelf life of the product and survival in the gastrointestinal (GI) tract to populate the human gut are two important issues in health benefit provision by probiotics. Additionally, factors related to the technological and sensory aspects of probiotic food production are of importance since only by satisfying the demands of consumers can the food industry succeed in promoting the consumption of functional probiotic products in the future. In the past, microorganisms were immobilized or entrapped in polymer matrices for use in food and biotechnological applications. As the technique of immobilization or entrapment became refined, the immobilized cell technology has evolved into encapsulation of cells. Compared to immobilization/entrapment techniques, microencapsulation (ME) has many advantages. There are several methods of ME. However, technologies applied to probiotics are generally limited to gelling, spray-drying, spray-cooling, extrusion, and emulsions. Controlled release of bacteria is a critical benefit of ME. As clinical evidence of the beneficial effects of probiotics accumulates, the food, nutraceutical, and pharmaceutical industries will formulate new and innovative probiotic-based therapeutic products.

Campylobacter infections in humans are considered to be mainly food-borne, in which foods of animal origin play an important role. The majority of Campylobacter infections are sporadic (single) cases or small family outbreaks, and the actual source of these types of infection is rarely microbiologically identified. This chapter describes the detection and prevalence of Campylobacter in a wide range of different types of food. Food products, however, may harbor only low numbers of campylobacters, and bacterial cells may be seriously injured by processing procedures such as freezing, cooling, heating, and salting. Survival of Campylobacter on eggshells, however, is considered to be poor because of the sensitivity of the organism to drying. Unpasteurized milk is a well-documented cause of a number of outbreaks of campylobacteriosis. Sufficient heating of red meat products, which are relatively infrequently contaminated with low numbers of Campylobacter, will eliminate this risk of human infection. Several investigations on the detection of Campylobacter in different types of seafood have been carried out. The majority of Campylobacter studies on growth characteristics and survival were carried out during the early 1980s, and summarizing reviews can be found in articles by Doyle and Stern and Kazmi. Reduction of the potential risk of contaminated poultry products has to be achieved by the application of good hygienic practices by both the producers of poultry meat products and the consumers of these products.

This chapter describes the interactions of microorganisms with dairy foods that lead to commonly encountered product defects. The major microbial inhibitors in raw milk are lactoferrin and the lactoperoxidase system. Fluid milk, cheese, and cultured milks are the major dairy products susceptible to spoilage by non-spore-forming fermentative bacteria. Non-spore-forming bacteria responsible for fermentative spoilage of dairy products are mostly in either the lactic acid-producing or coliform group. The most common fermentative defect in fluid milk products is souring caused by the growth of lactic acid bacteria. The defect in noncultured fluid milk products is usually caused by growth of specific strains of lactococci. Spore-forming bacteria that spoil dairy products usually originate in the raw milk. The defect in milk products is described as sweet curdling, since it first appears as coagulation without significant acid or off flavor being formed. The major heat-resistant species in milk is Geobacillus stearothermophilus (formerly Bacillus stearothermophilus). A practical means to prevent sporeformers from spoiling nonfermented liquid dairy products given sub-ultrahigh-temperature (UHT) heat treatments has not been developed. The most common yeasts present in dairy products are Kluyveromyces marxianus and Debaryomyces hansenii (the teleomorph) and their asporogenous counterparts (the anamorph), Candida species, and Zygosaccharomyces microellipsoides. Yeasts and molds that spoil dairy products can usually be isolated in the processing plant on packaging equipment, in the air, in salt brine, on manufacturing equipment, and in the general environment (floors, walls, ventilation ducts, etc.).

The primary microflora used in the production of fermented milk products are the homofermentative lactic acid bacteria (LAB). Additionally, yeasts, molds, and several other species of bacteria, including heterofermentative LAB, may be added to specific products; however, their purpose is not for acid development but for the production of flavor components or carbon dioxide. In some fermented dairy products, additional bacteria, often referred to as secondary microflora (but essential to flavor development), are added to influence flavor and alter texture of the final product. The use of nonstarter LAB, especially lactobacilli, as adjunct flavor cultures is a burgeoning research area and is practiced commercially. Proteolytic systems in LAB contribute to their ability to grow in milk and are necessary for the development of flavor in ripened cheeses. The production of high-quality fermented dairy products is dependent on the proteolytic systems of LAB. Bacteriophage infection may lead to a decrease or complete inhibition of lactic acid production by the starter culture. This has a major impact on the manufacture of fermented dairy products, as lactic acid synthesis is required to produce these products. Researchers have begun to characterize host components required for bacteriophage adsorption. It is now thought that bacteriophages initially interact reversibly with cell envelope-associated polysaccharide and then interact irreversibly with cell membrane protein(s).